I've read that the amoeba is capable of learning. Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the ...

Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or ...

I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...

After looking at this question, some other questions poped in my mind.
The DNA code is redundant, there are 20 amino acids for 64 possible nucleotide combinations. Therefore some amino acid are coded ...

We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic ...

Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based ...

Every bloody protocol suggests adding in DTT when doing in vitro RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein ...

I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...

Before anything else please pay attention of the double quotes on the "equal" in the title - I know they are not equal, but you will understand in a bit.
If I look at the DNA codon table here or in ...

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...

I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control ...

Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of in vitro or in silico tries to find correct reading frame of a sequence?
Is it just ...

According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.
How are these micro-lesions ...

My book keeps giving different indicators as to whether the promoters are on the coding or template strand.
It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene:
One of the simplest ways to model GFP transcription is to use an ODE:
$\frac{d [GFP_{mRNA}]}{dt} = a - ...

I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...

What is the trigger for DNA to produce proteins or RNA?
I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...

In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second.
Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs?
...

If the sole known function of a gene is to activate a transcription factor, would that gene also be considered a transcription factor, or is there a word for such genes that are further upstream on ...

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites).
The motifs belong to several species, and I wanted to cluster these ...

I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting ...

CpG content varies a lot across the human genome. What does determine a promoter to be silenced through DNA methylation: the fraction of CpG sites that are methylated or the total number of methylated ...

I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one ...

When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? ...

This article gives measurement of transcription rate and the unit they're using is microarray per hour.
For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...

I have noticed that some TF binding sites are located in the introns of the genes.
I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during ...

For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing). Does the cell differentiate between these DNA in any way or are transcription ...

I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by ...